Since the Appeal Board gave no reason for the denial of a conscientious objector exemption to petitioner, and it is impossible to determine on which of the three grounds offered in the Justice Department's letter that board relied, petitioner's conviction must be reversed.

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In 1964, Ali failed the U.S. Armed Forces qualifying test because his writing and spelling skills were sub-standard. With the escalation of the Vietnam War, the test standards were lowered in November 1965[4] and Ali was reclassified as 1-A in February 1966,[5][6] which meant he was now eligible for the draft and induction into the U.S. Army. When notified of this status, he declared that he would refuse to serve in the U.S. Army and publicly considered himself a conscientious objector. Ali stated that "War is against the teachings of the Holy Qur'an. I'm not trying to dodge the draft. We are not supposed to take part in no wars unless declared by Allah or The Messenger. We don't take part in Christian wars or wars of any unbelievers." Ali also famously said in 1966: "I ain't got no quarrel with them Viet Cong ... They never called me nigger."[7][8]

Ali appealed his local (Louisville, Kentucky) draft board's rejection of his application for conscientious objector classification.[9] The Justice Department, in response to the State Appeal Board's referral for an advisory recommendation, concluded, contrary to a hearing officer's recommendation, that Ali's claim should be denied, and wrote that board that Ali did not meet any of the three basic tests for conscientious objector status. The Appeal Board then denied Ali's claim, but without stating its reasons.

In early 1967, Ali changed his legal residence to Houston, Texas,[10][11] where his appeal to be reclassified as a Muslim minister was denied 4-0 by the federal judicial district on February 20.[12] He appeared for his scheduled induction into the U.S. Armed Forces on in Houston on April 28. As expected, Ali refused three times to step forward at the call of his name. An officer warned him he was committing a felony punishable by five years in prison and a fine of $10,000. Once more, Ali refused to budge when his name was called. As a result, on that same day, the New York State Athletic Commission suspended his boxing license and the World Boxing Association stripped him of his title.[13][14] Other boxing commissions followed suit. He was indicted by a federal grand jury on May 8[15] and convicted in Houston on June 20.[16][17] The trial jury was composed of six men and six women, all of whom were white.[18] The Court of Appeals affirmed and denied the appeal on May 6, 1968.[19]

In the U.S. Supreme Court, the government conceded the invalidity of two of the grounds for denial of petitioner's claim given in its letter to the appeal board, but argued that there was factual support for the third ground.

The Supreme Court held that, since the appeal board gave no reason for the denial of a conscientious objector exemption to petitioner, and it is impossible to determine on which of the three grounds offered in the Justice Department's letter that board relied, Ali's 1967 conviction must be reversed. The Supreme Court decision was handed down on June 28, 1971.[2][3][20]

Bob Woodward and Scott Armstrong provide an account of the development of the decision in their book The Brethren. According to that account, Justice Marshall had recused himself because he had been U.S. Solicitor General when the case began, and the remaining eight justices initially voted 5 to 3 to uphold Ali's conviction. However, Justice Harlan, assigned to write the majority opinion, became convinced that Ali's claim to be a conscientious objector was sincere after reading background material on Black Muslim doctrine provided by one of his law clerks. To the contrary, Justice Harlan concluded that the claim by the Justice Department had been a misrepresentation. Harlan changed his vote, tying the vote at 4 to 4. A deadlock would have resulted in Ali being jailed for draft evasion and, since no opinions are published for deadlocked decisions, he would have never known why he had lost. A compromise proposed by Justice Stewart, in which Ali's conviction would be reversed citing a technical error by the Justice Department, gradually won unanimous assent from the eight voting justices.[21]